cansas_reader.py @ 18f11a6

ESS_GUIESS_GUI_batch_fittingESS_GUI_bumps_abstractionESS_GUI_iss1116ESS_GUI_iss879ESS_GUI_openclESS_GUI_orderingESS_GUI_sync_sascalc

Last change on this file since 18f11a6 was 2b538cd, checked in by krzywon, 7 years ago
Modify documentation and add instance check for numpy arrays in HDF5 reader.
Property mode set to `100644`
File size: 61.3 KB

Line
1	import logging
2	import os
3	import sys
4	import datetime
5	import inspect
6
7	import numpy as np
8
9	# The following 2 imports ARE used. Do not remove either.
10	import xml.dom.minidom
11	from xml.dom.minidom import parseString
12
13	from lxml import etree
14
15	from sas.sascalc.data_util.nxsunit import Converter
16
17	# For saving individual sections of data
18	from ..data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D, \
19	Collimation, TransmissionSpectrum, Detector, Process, Aperture, \
20	combine_data_info_with_plottable as combine_data
21	from ..loader_exceptions import FileContentsException, DefaultReaderException, \
22	DataReaderException
23	from . import xml_reader
24	from .xml_reader import XMLreader
25	from .cansas_constants import CansasConstants, CurrentLevel
26
27	logger = logging.getLogger(__name__)
28
29	PREPROCESS = "xmlpreprocess"
30	ENCODING = "encoding"
31	RUN_NAME_DEFAULT = "None"
32	INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
33	INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
34	INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
35	"as much of the data as possible.\n\n"
36
37	CONSTANTS = CansasConstants()
38	CANSAS_FORMAT = CONSTANTS.format
39	CANSAS_NS = CONSTANTS.names
40	ALLOW_ALL = True
41
42	class Reader(XMLreader):
43	cansas_version = "1.0"
44	base_ns = "{cansas1d/1.0}"
45	cansas_defaults = None
46	type_name = "canSAS"
47	invalid = True
48	frm = ""
49	# Log messages and errors
50	logging = None
51	errors = set()
52	# Namespace hierarchy for current xml_file object
53	names = None
54	ns_list = None
55	# Temporary storage location for loading multiple data sets in a single file
56	current_data1d = None
57	data = None
58	# Wildcards
59	type = ["XML files (.xml)\|.xml", "SasView Save Files (.svs)\|.svs"]
60	# List of allowed extensions
61	ext = ['.xml', '.XML', '.svs', '.SVS']
62	# Flag to bypass extension check
63	allow_all = True
64
65	def reset_state(self):
66	"""
67	Resets the class state to a base case when loading a new data file so previous
68	data files do not appear a second time
69	"""
70	self.current_datainfo = None
71	self.current_dataset = None
72	self.current_data1d = None
73	self.data = []
74	self.process = Process()
75	self.transspectrum = TransmissionSpectrum()
76	self.aperture = Aperture()
77	self.collimation = Collimation()
78	self.detector = Detector()
79	self.names = []
80	self.cansas_defaults = {}
81	self.output = []
82	self.ns_list = None
83	self.logging = []
84	self.encoding = None
85
86	def read(self, xml_file, schema_path="", invalid=True):
87	if schema_path != "" or invalid != True:
88	# read has been called from self.get_file_contents because xml file doens't conform to schema
89	_, self.extension = os.path.splitext(os.path.basename(xml_file))
90	return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
91
92	# Otherwise, read has been called by the data loader - file_reader_base_class handles this
93	return super(XMLreader, self).read(xml_file)
94
95	def get_file_contents(self, xml_file=None, schema_path="", invalid=True):
96	# Reset everything since we're loading a new file
97	self.reset_state()
98	self.invalid = invalid
99	if xml_file is None:
100	xml_file = self.f_open.name
101	# We don't sure f_open since lxml handles opnening/closing files
102	try:
103	# Raises FileContentsException
104	self.load_file_and_schema(xml_file, schema_path)
105	# Parse each SASentry
106	entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry',
107	namespaces={
108	'ns': self.cansas_defaults.get(
109	"ns")
110	})
111	self.is_cansas(self.extension)
112	self.set_processing_instructions()
113	for entry in entry_list:
114	self._parse_entry(entry)
115	self.data_cleanup()
116	except FileContentsException as fc_exc:
117	# File doesn't meet schema - try loading with a less strict schema
118	base_name = xml_reader.__file__
119	base_name = base_name.replace("\\", "/")
120	base = base_name.split("/sas/")[0]
121	if self.cansas_version == "1.1":
122	invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
123	else:
124	invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
125	self.set_schema(invalid_schema)
126	if self.invalid:
127	try:
128	# Load data with less strict schema
129	self.read(xml_file, invalid_schema, False)
130
131	# File can still be read but doesn't match schema, so raise exception
132	self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
133	invalid_xml = self.find_invalid_xml()
134	if invalid_xml != "":
135	basename, _ = os.path.splitext(
136	os.path.basename(self.f_open.name))
137	invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
138	raise DataReaderException(invalid_xml) # Handled by base class
139	except FileContentsException as fc_exc:
140	msg = "CanSAS Reader could not load the file {}".format(xml_file)
141	if fc_exc.message is not None: # Propagate error messages from earlier
142	msg = fc_exc.message
143	if not self.extension in self.ext: # If the file has no associated loader
144	raise DefaultReaderException(msg)
145	raise FileContentsException(msg)
146	pass
147	else:
148	raise fc_exc
149	except Exception as e: # Convert all other exceptions to FileContentsExceptions
150	raise FileContentsException(str(e))
151	finally:
152	if not self.f_open.closed:
153	self.f_open.close()
154
155	def load_file_and_schema(self, xml_file, schema_path=""):
156	base_name = xml_reader.__file__
157	base_name = base_name.replace("\\", "/")
158	base = base_name.split("/sas/")[0]
159
160	# Try and parse the XML file
161	try:
162	self.set_xml_file(xml_file)
163	except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
164	msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
165	raise FileContentsException(msg)
166
167	self.cansas_version = self.xmlroot.get("version", "1.0")
168	self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
169
170	if schema_path == "":
171	schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
172	base, self.cansas_defaults.get("schema").replace("\\", "/")
173	)
174	self.set_schema(schema_path)
175
176	def is_cansas(self, ext="xml"):
177	"""
178	Checks to see if the XML file is a CanSAS file
179
180	:param ext: The file extension of the data file
181	:raises FileContentsException: Raised if XML file isn't valid CanSAS
182	"""
183	if self.validate_xml(): # Check file is valid XML
184	name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
185	value = self.xmlroot.get(name)
186	# Check schema CanSAS version matches file CanSAS version
187	if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
188	return True
189	if ext == "svs":
190	return True # Why is this required?
191	# If we get to this point then file isn't valid CanSAS
192	logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
193	raise FileContentsException("The file is not valid CanSAS")
194
195	def _parse_entry(self, dom, recurse=False):
196	if not self._is_call_local() and not recurse:
197	self.reset_state()
198	if not recurse:
199	self.current_datainfo = DataInfo()
200	# Raises FileContentsException if file doesn't meet CanSAS schema
201	self.invalid = False
202	# Look for a SASentry
203	self.data = []
204	self.parent_class = "SASentry"
205	self.names.append("SASentry")
206	self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
207	self.current_datainfo.meta_data[
208	PREPROCESS] = self.processing_instructions
209	if self._is_call_local() and not recurse:
210	basename, _ = os.path.splitext(os.path.basename(self.f_open.name))
211	self.current_datainfo.filename = basename + self.extension
212	# Create an empty dataset if no data has been passed to the reader
213	if self.current_dataset is None:
214	self._initialize_new_data_set(dom)
215	self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
216
217	# Loop through each child in the parent element
218	for node in dom:
219	attr = node.attrib
220	name = attr.get("name", "")
221	type = attr.get("type", "")
222	# Get the element name and set the current names level
223	tagname = node.tag.replace(self.base_ns, "")
224	tagname_original = tagname
225	# Skip this iteration when loading in save state information
226	if tagname in ["fitting_plug_in", "pr_inversion", "invariant", "corfunc"]:
227	continue
228	# Get where to store content
229	self.names.append(tagname_original)
230	self.ns_list = CONSTANTS.iterate_namespace(self.names)
231	# If the element is a child element, recurse
232	if len(node.getchildren()) > 0:
233	self.parent_class = tagname_original
234	if tagname == 'SASdata':
235	self._initialize_new_data_set(node)
236	if isinstance(self.current_dataset, plottable_2D):
237	x_bins = attr.get("x_bins", "")
238	y_bins = attr.get("y_bins", "")
239	if x_bins is not "" and y_bins is not "":
240	self.current_dataset.shape = (x_bins, y_bins)
241	else:
242	self.current_dataset.shape = ()
243	# Recurse to access data within the group
244	self._parse_entry(node, recurse=True)
245	if tagname == "SASsample":
246	self.current_datainfo.sample.name = name
247	elif tagname == "beam_size":
248	self.current_datainfo.source.beam_size_name = name
249	elif tagname == "SAScollimation":
250	self.collimation.name = name
251	elif tagname == "aperture":
252	self.aperture.name = name
253	self.aperture.type = type
254	self._add_intermediate()
255	else:
256	# TODO: Clean this up to make it faster (fewer if/elifs)
257	if isinstance(self.current_dataset, plottable_2D):
258	data_point = node.text
259	unit = attr.get('unit', '')
260	else:
261	data_point, unit = self._get_node_value(node, tagname)
262
263	# If this is a dataset, store the data appropriately
264	if tagname == 'Run':
265	self.current_datainfo.run_name[data_point] = name
266	self.current_datainfo.run.append(data_point)
267	elif tagname == 'Title':
268	self.current_datainfo.title = data_point
269	elif tagname == 'SASnote':
270	self.current_datainfo.notes.append(data_point)
271
272	# I and Q points
273	elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
274	self.current_dataset.yaxis("Intensity", unit)
275	self.current_dataset.y = np.append(self.current_dataset.y, data_point)
276	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
277	self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
278	elif tagname == 'Q':
279	self.current_dataset.xaxis("Q", unit)
280	self.current_dataset.x = np.append(self.current_dataset.x, data_point)
281	elif tagname == 'Qdev':
282	self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
283	elif tagname == 'dQw':
284	self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
285	elif tagname == 'dQl':
286	self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
287	elif tagname == 'Qmean':
288	pass
289	elif tagname == 'Shadowfactor':
290	pass
291	elif tagname == 'Sesans':
292	self.current_datainfo.isSesans = bool(data_point)
293	self.current_dataset.xaxis(attr.get('x_axis'),
294	attr.get('x_unit'))
295	self.current_dataset.yaxis(attr.get('y_axis'),
296	attr.get('y_unit'))
297	elif tagname == 'yacceptance':
298	self.current_datainfo.sample.yacceptance = (data_point, unit)
299	elif tagname == 'zacceptance':
300	self.current_datainfo.sample.zacceptance = (data_point, unit)
301
302	# I and Qx, Qy - 2D data
303	elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
304	self.current_dataset.yaxis("Intensity", unit)
305	self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
306	elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
307	self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
308	elif tagname == 'Qx':
309	self.current_dataset.xaxis("Qx", unit)
310	self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
311	elif tagname == 'Qy':
312	self.current_dataset.yaxis("Qy", unit)
313	self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
314	elif tagname == 'Qxdev':
315	self.current_dataset.xaxis("Qxdev", unit)
316	self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
317	elif tagname == 'Qydev':
318	self.current_dataset.yaxis("Qydev", unit)
319	self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
320	elif tagname == 'Mask':
321	inter = [item == "1" for item in data_point.split(",")]
322	self.current_dataset.mask = np.asarray(inter, dtype=bool)
323
324	# Sample Information
325	elif tagname == 'ID' and self.parent_class == 'SASsample':
326	self.current_datainfo.sample.ID = data_point
327	elif tagname == 'Title' and self.parent_class == 'SASsample':
328	self.current_datainfo.sample.name = data_point
329	elif tagname == 'thickness' and self.parent_class == 'SASsample':
330	self.current_datainfo.sample.thickness = data_point
331	self.current_datainfo.sample.thickness_unit = unit
332	elif tagname == 'transmission' and self.parent_class == 'SASsample':
333	self.current_datainfo.sample.transmission = data_point
334	elif tagname == 'temperature' and self.parent_class == 'SASsample':
335	self.current_datainfo.sample.temperature = data_point
336	self.current_datainfo.sample.temperature_unit = unit
337	elif tagname == 'details' and self.parent_class == 'SASsample':
338	self.current_datainfo.sample.details.append(data_point)
339	elif tagname == 'x' and self.parent_class == 'position':
340	self.current_datainfo.sample.position.x = data_point
341	self.current_datainfo.sample.position_unit = unit
342	elif tagname == 'y' and self.parent_class == 'position':
343	self.current_datainfo.sample.position.y = data_point
344	self.current_datainfo.sample.position_unit = unit
345	elif tagname == 'z' and self.parent_class == 'position':
346	self.current_datainfo.sample.position.z = data_point
347	self.current_datainfo.sample.position_unit = unit
348	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
349	self.current_datainfo.sample.orientation.x = data_point
350	self.current_datainfo.sample.orientation_unit = unit
351	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
352	self.current_datainfo.sample.orientation.y = data_point
353	self.current_datainfo.sample.orientation_unit = unit
354	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
355	self.current_datainfo.sample.orientation.z = data_point
356	self.current_datainfo.sample.orientation_unit = unit
357
358	# Instrumental Information
359	elif tagname == 'name' and self.parent_class == 'SASinstrument':
360	self.current_datainfo.instrument = data_point
361
362	# Detector Information
363	elif tagname == 'name' and self.parent_class == 'SASdetector':
364	self.detector.name = data_point
365	elif tagname == 'SDD' and self.parent_class == 'SASdetector':
366	self.detector.distance = data_point
367	self.detector.distance_unit = unit
368	elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
369	self.detector.slit_length = data_point
370	self.detector.slit_length_unit = unit
371	elif tagname == 'x' and self.parent_class == 'offset':
372	self.detector.offset.x = data_point
373	self.detector.offset_unit = unit
374	elif tagname == 'y' and self.parent_class == 'offset':
375	self.detector.offset.y = data_point
376	self.detector.offset_unit = unit
377	elif tagname == 'z' and self.parent_class == 'offset':
378	self.detector.offset.z = data_point
379	self.detector.offset_unit = unit
380	elif tagname == 'x' and self.parent_class == 'beam_center':
381	self.detector.beam_center.x = data_point
382	self.detector.beam_center_unit = unit
383	elif tagname == 'y' and self.parent_class == 'beam_center':
384	self.detector.beam_center.y = data_point
385	self.detector.beam_center_unit = unit
386	elif tagname == 'z' and self.parent_class == 'beam_center':
387	self.detector.beam_center.z = data_point
388	self.detector.beam_center_unit = unit
389	elif tagname == 'x' and self.parent_class == 'pixel_size':
390	self.detector.pixel_size.x = data_point
391	self.detector.pixel_size_unit = unit
392	elif tagname == 'y' and self.parent_class == 'pixel_size':
393	self.detector.pixel_size.y = data_point
394	self.detector.pixel_size_unit = unit
395	elif tagname == 'z' and self.parent_class == 'pixel_size':
396	self.detector.pixel_size.z = data_point
397	self.detector.pixel_size_unit = unit
398	elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
399	self.detector.orientation.x = data_point
400	self.detector.orientation_unit = unit
401	elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
402	self.detector.orientation.y = data_point
403	self.detector.orientation_unit = unit
404	elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
405	self.detector.orientation.z = data_point
406	self.detector.orientation_unit = unit
407
408	# Collimation and Aperture
409	elif tagname == 'length' and self.parent_class == 'SAScollimation':
410	self.collimation.length = data_point
411	self.collimation.length_unit = unit
412	elif tagname == 'name' and self.parent_class == 'SAScollimation':
413	self.collimation.name = data_point
414	elif tagname == 'distance' and self.parent_class == 'aperture':
415	self.aperture.distance = data_point
416	self.aperture.distance_unit = unit
417	elif tagname == 'x' and self.parent_class == 'size':
418	self.aperture.size.x = data_point
419	self.collimation.size_unit = unit
420	elif tagname == 'y' and self.parent_class == 'size':
421	self.aperture.size.y = data_point
422	self.collimation.size_unit = unit
423	elif tagname == 'z' and self.parent_class == 'size':
424	self.aperture.size.z = data_point
425	self.collimation.size_unit = unit
426
427	# Process Information
428	elif tagname == 'name' and self.parent_class == 'SASprocess':
429	self.process.name = data_point
430	elif tagname == 'description' and self.parent_class == 'SASprocess':
431	self.process.description = data_point
432	elif tagname == 'date' and self.parent_class == 'SASprocess':
433	try:
434	self.process.date = datetime.datetime.fromtimestamp(data_point)
435	except:
436	self.process.date = data_point
437	elif tagname == 'SASprocessnote':
438	self.process.notes.append(data_point)
439	elif tagname == 'term' and self.parent_class == 'SASprocess':
440	unit = attr.get("unit", "")
441	dic = { "name": name, "value": data_point, "unit": unit }
442	self.process.term.append(dic)
443
444	# Transmission Spectrum
445	elif tagname == 'T' and self.parent_class == 'Tdata':
446	self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
447	self.transspectrum.transmission_unit = unit
448	elif tagname == 'Tdev' and self.parent_class == 'Tdata':
449	self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
450	self.transspectrum.transmission_deviation_unit = unit
451	elif tagname == 'Lambda' and self.parent_class == 'Tdata':
452	self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
453	self.transspectrum.wavelength_unit = unit
454
455	# Source Information
456	elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
457	self.current_datainfo.source.wavelength = data_point
458	self.current_datainfo.source.wavelength_unit = unit
459	elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
460	self.current_datainfo.source.wavelength_min = data_point
461	self.current_datainfo.source.wavelength_min_unit = unit
462	elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
463	self.current_datainfo.source.wavelength_max = data_point
464	self.current_datainfo.source.wavelength_max_unit = unit
465	elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
466	self.current_datainfo.source.wavelength_spread = data_point
467	self.current_datainfo.source.wavelength_spread_unit = unit
468	elif tagname == 'x' and self.parent_class == 'beam_size':
469	self.current_datainfo.source.beam_size.x = data_point
470	self.current_datainfo.source.beam_size_unit = unit
471	elif tagname == 'y' and self.parent_class == 'beam_size':
472	self.current_datainfo.source.beam_size.y = data_point
473	self.current_datainfo.source.beam_size_unit = unit
474	elif tagname == 'z' and self.parent_class == 'pixel_size':
475	self.current_datainfo.source.data_point.z = data_point
476	self.current_datainfo.source.beam_size_unit = unit
477	elif tagname == 'radiation' and self.parent_class == 'SASsource':
478	self.current_datainfo.source.radiation = data_point
479	elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
480	self.current_datainfo.source.beam_shape = data_point
481
482	# Everything else goes in meta_data
483	else:
484	new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
485	self.current_datainfo.meta_data[new_key] = data_point
486
487	self.names.remove(tagname_original)
488	length = 0
489	if len(self.names) > 1:
490	length = len(self.names) - 1
491	self.parent_class = self.names[length]
492	if not self._is_call_local() and not recurse:
493	self.frm = ""
494	self.current_datainfo.errors = set()
495	for error in self.errors:
496	self.current_datainfo.errors.add(error)
497	self.data_cleanup()
498	self.sort_one_d_data()
499	self.sort_two_d_data()
500	self.reset_data_list()
501	return self.output[0], None
502
503	def _is_call_local(self):
504	if self.frm == "":
505	inter = inspect.stack()
506	self.frm = inter[2]
507	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
508	mod_name = mod_name.replace(".py", "")
509	mod = mod_name.split("sas/")
510	mod_name = mod[1]
511	if mod_name != "sascalc/dataloader/readers/cansas_reader":
512	return False
513	return True
514
515	def _add_intermediate(self):
516	"""
517	This method stores any intermediate objects within the final data set after fully reading the set.
518	"""
519	if self.parent_class == 'SASprocess':
520	self.current_datainfo.process.append(self.process)
521	self.process = Process()
522	elif self.parent_class == 'SASdetector':
523	self.current_datainfo.detector.append(self.detector)
524	self.detector = Detector()
525	elif self.parent_class == 'SAStransmission_spectrum':
526	self.current_datainfo.trans_spectrum.append(self.transspectrum)
527	self.transspectrum = TransmissionSpectrum()
528	elif self.parent_class == 'SAScollimation':
529	self.current_datainfo.collimation.append(self.collimation)
530	self.collimation = Collimation()
531	elif self.parent_class == 'aperture':
532	self.collimation.aperture.append(self.aperture)
533	self.aperture = Aperture()
534	elif self.parent_class == 'SASdata':
535	self.data.append(self.current_dataset)
536
537	def _get_node_value(self, node, tagname):
538	"""
539	Get the value of a node and any applicable units
540
541	:param node: The XML node to get the value of
542	:param tagname: The tagname of the node
543	"""
544	#Get the text from the node and convert all whitespace to spaces
545	units = ''
546	node_value = node.text
547	if node_value is not None:
548	node_value = ' '.join(node_value.split())
549	else:
550	node_value = ""
551
552	# If the value is a float, compile with units.
553	if self.ns_list.ns_datatype == "float":
554	# If an empty value is given, set as zero.
555	if node_value is None or node_value.isspace() \
556	or node_value.lower() == "nan":
557	node_value = "0.0"
558	#Convert the value to the base units
559	node_value, units = self._unit_conversion(node, tagname, node_value)
560
561	# If the value is a timestamp, convert to a datetime object
562	elif self.ns_list.ns_datatype == "timestamp":
563	if node_value is None or node_value.isspace():
564	pass
565	else:
566	try:
567	node_value = \
568	datetime.datetime.fromtimestamp(node_value)
569	except ValueError:
570	node_value = None
571	return node_value, units
572
573	def _unit_conversion(self, node, tagname, node_value):
574	"""
575	A unit converter method used to convert the data included in the file
576	to the default units listed in data_info
577
578	:param node: XML node
579	:param tagname: name of the node
580	:param node_value: The value of the current dom node
581	"""
582	attr = node.attrib
583	value_unit = ''
584	err_msg = None
585	default_unit = None
586	if not isinstance(node_value, float):
587	node_value = float(node_value)
588	if 'unit' in attr and attr.get('unit') is not None:
589	try:
590	unit = attr['unit']
591	# Split the units to retain backwards compatibility with
592	# projects, analyses, and saved data from v4.1.0
593	unit_list = unit.split("\|")
594	if len(unit_list) > 1:
595	local_unit = unit_list[1]
596	else:
597	local_unit = unit
598	unitname = self.ns_list.current_level.get("unit", "")
599	if "SASdetector" in self.names:
600	save_in = "detector"
601	elif "aperture" in self.names:
602	save_in = "aperture"
603	elif "SAScollimation" in self.names:
604	save_in = "collimation"
605	elif "SAStransmission_spectrum" in self.names:
606	save_in = "transspectrum"
607	elif "SASdata" in self.names:
608	x = np.zeros(1)
609	y = np.zeros(1)
610	self.current_data1d = Data1D(x, y)
611	save_in = "current_data1d"
612	elif "SASsource" in self.names:
613	save_in = "current_datainfo.source"
614	elif "SASsample" in self.names:
615	save_in = "current_datainfo.sample"
616	elif "SASprocess" in self.names:
617	save_in = "process"
618	else:
619	save_in = "current_datainfo"
620	default_unit = getattrchain(self, '.'.join((save_in, unitname)))
621	if (local_unit and default_unit
622	and local_unit.lower() != default_unit.lower()
623	and local_unit.lower() != "none"):
624	# Check local units - bad units raise KeyError
625	#print("loading", tagname, node_value, local_unit, default_unit)
626	data_conv_q = Converter(local_unit)
627	value_unit = default_unit
628	node_value = data_conv_q(node_value, units=default_unit)
629	else:
630	value_unit = local_unit
631	except KeyError:
632	# Do not throw an error for loading Sesans data in cansas xml
633	# This is a temporary fix.
634	if local_unit != "A" and local_unit != 'pol':
635	err_msg = "CanSAS reader: unexpected "
636	err_msg += "\"{0}\" unit [{1}]; "
637	err_msg = err_msg.format(tagname, local_unit)
638	err_msg += "expecting [{0}]".format(default_unit)
639	value_unit = local_unit
640	except Exception:
641	err_msg = "CanSAS reader: unknown error converting "
642	err_msg += "\"{0}\" unit [{1}]"
643	err_msg = err_msg.format(tagname, local_unit)
644	value_unit = local_unit
645	elif 'unit' in attr:
646	value_unit = attr['unit']
647	if err_msg:
648	self.errors.add(err_msg)
649	return node_value, value_unit
650
651	def _initialize_new_data_set(self, node=None):
652	if node is not None:
653	for child in node:
654	if child.tag.replace(self.base_ns, "") == "Idata":
655	for i_child in child:
656	if i_child.tag.replace(self.base_ns, "") == "Qx":
657	self.current_dataset = plottable_2D()
658	return
659	self.current_dataset = plottable_1D(np.array(0), np.array(0))
660
661	## Writing Methods
662	def write(self, filename, datainfo):
663	"""
664	Write the content of a Data1D as a CanSAS XML file
665
666	:param filename: name of the file to write
667	:param datainfo: Data1D object
668	"""
669	# Create XML document
670	doc, _ = self._to_xml_doc(datainfo)
671	# Write the file
672	file_ref = open(filename, 'wb')
673	if self.encoding is None:
674	self.encoding = "UTF-8"
675	doc.write(file_ref, encoding=self.encoding,
676	pretty_print=True, xml_declaration=True)
677	file_ref.close()
678
679	def _to_xml_doc(self, datainfo):
680	"""
681	Create an XML document to contain the content of a Data1D
682
683	:param datainfo: Data1D object
684	"""
685	is_2d = False
686	if issubclass(datainfo.__class__, Data2D):
687	is_2d = True
688
689	# Get PIs and create root element
690	pi_string = self._get_pi_string()
691	# Define namespaces and create SASroot object
692	main_node = self._create_main_node()
693	# Create ElementTree, append SASroot and apply processing instructions
694	base_string = pi_string + self.to_string(main_node)
695	base_element = self.create_element_from_string(base_string)
696	doc = self.create_tree(base_element)
697	# Create SASentry Element
698	entry_node = self.create_element("SASentry")
699	root = doc.getroot()
700	root.append(entry_node)
701
702	# Add Title to SASentry
703	self.write_node(entry_node, "Title", datainfo.title)
704	# Add Run to SASentry
705	self._write_run_names(datainfo, entry_node)
706	# Add Data info to SASEntry
707	if is_2d:
708	self._write_data_2d(datainfo, entry_node)
709	else:
710	self._write_data(datainfo, entry_node)
711	# Transmission Spectrum Info
712	# TODO: fix the writer to linearize all data, including T_spectrum
713	# self._write_trans_spectrum(datainfo, entry_node)
714	# Sample info
715	self._write_sample_info(datainfo, entry_node)
716	# Instrument info
717	instr = self._write_instrument(datainfo, entry_node)
718	# Source
719	self._write_source(datainfo, instr)
720	# Collimation
721	self._write_collimation(datainfo, instr)
722	# Detectors
723	self._write_detectors(datainfo, instr)
724	# Processes info
725	self._write_process_notes(datainfo, entry_node)
726	# Note info
727	self._write_notes(datainfo, entry_node)
728	# Return the document, and the SASentry node associated with
729	# the data we just wrote
730	# If the calling function was not the cansas reader, return a minidom
731	# object rather than an lxml object.
732	self.frm = inspect.stack()[1]
733	doc, entry_node = self._check_origin(entry_node, doc)
734	return doc, entry_node
735
736	def write_node(self, parent, name, value, attr=None):
737	"""
738	:param doc: document DOM
739	:param parent: parent node
740	:param name: tag of the element
741	:param value: value of the child text node
742	:param attr: attribute dictionary
743
744	:return: True if something was appended, otherwise False
745	"""
746	if value is not None:
747	parent = self.ebuilder(parent, name, value, attr)
748	return True
749	return False
750
751	def _get_pi_string(self):
752	"""
753	Creates the processing instructions header for writing to file
754	"""
755	pis = self.return_processing_instructions()
756	if len(pis) > 0:
757	pi_tree = self.create_tree(pis[0])
758	i = 1
759	for i in range(1, len(pis) - 1):
760	pi_tree = self.append(pis[i], pi_tree)
761	pi_string = self.to_string(pi_tree)
762	else:
763	pi_string = ""
764	return pi_string
765
766	def _create_main_node(self):
767	"""
768	Creates the primary xml header used when writing to file
769	"""
770	xsi = "http://www.w3.org/2001/XMLSchema-instance"
771	version = self.cansas_version
772	n_s = CANSAS_NS.get(version).get("ns")
773	if version == "1.1":
774	url = "http://www.cansas.org/formats/1.1/"
775	else:
776	url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
777	schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
778	attrib = {"{" + xsi + "}schemaLocation" : schema_location,
779	"version" : version}
780	nsmap = {'xsi' : xsi, None: n_s}
781
782	main_node = self.create_element("{" + n_s + "}SASroot",
783	attrib=attrib, nsmap=nsmap)
784	return main_node
785
786	def _write_run_names(self, datainfo, entry_node):
787	"""
788	Writes the run names to the XML file
789
790	:param datainfo: The Data1D object the information is coming from
791	:param entry_node: lxml node ElementTree object to be appended to
792	"""
793	if datainfo.run is None or datainfo.run == []:
794	datainfo.run.append(RUN_NAME_DEFAULT)
795	datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
796	for item in datainfo.run:
797	runname = {}
798	if item in datainfo.run_name and \
799	len(str(datainfo.run_name[item])) > 1:
800	runname = {'name': datainfo.run_name[item]}
801	self.write_node(entry_node, "Run", item, runname)
802
803	def _write_data(self, datainfo, entry_node):
804	"""
805	Writes 1D I and Q data to the XML file
806
807	:param datainfo: The Data1D object the information is coming from
808	:param entry_node: lxml node ElementTree object to be appended to
809	"""
810	node = self.create_element("SASdata")
811	self.append(node, entry_node)
812
813	for i in range(len(datainfo.x)):
814	point = self.create_element("Idata")
815	node.append(point)
816	self.write_node(point, "Q", datainfo.x[i],
817	{'unit': datainfo.x_unit})
818	if len(datainfo.y) >= i:
819	self.write_node(point, "I", datainfo.y[i],
820	{'unit': datainfo.y_unit})
821	if datainfo.dy is not None and len(datainfo.dy) > i:
822	self.write_node(point, "Idev", datainfo.dy[i],
823	{'unit': datainfo.y_unit})
824	if datainfo.dx is not None and len(datainfo.dx) > i:
825	self.write_node(point, "Qdev", datainfo.dx[i],
826	{'unit': datainfo.x_unit})
827	if datainfo.dxw is not None and len(datainfo.dxw) > i:
828	self.write_node(point, "dQw", datainfo.dxw[i],
829	{'unit': datainfo.x_unit})
830	if datainfo.dxl is not None and len(datainfo.dxl) > i:
831	self.write_node(point, "dQl", datainfo.dxl[i],
832	{'unit': datainfo.x_unit})
833	if datainfo.isSesans:
834	sesans_attrib = {'x_axis': datainfo._xaxis,
835	'y_axis': datainfo._yaxis,
836	'x_unit': datainfo.x_unit,
837	'y_unit': datainfo.y_unit}
838	sesans = self.create_element("Sesans", attrib=sesans_attrib)
839	sesans.text = str(datainfo.isSesans)
840	entry_node.append(sesans)
841	self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
842	{'unit': datainfo.sample.yacceptance[1]})
843	self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
844	{'unit': datainfo.sample.zacceptance[1]})
845
846
847	def _write_data_2d(self, datainfo, entry_node):
848	"""
849	Writes 2D data to the XML file
850
851	:param datainfo: The Data2D object the information is coming from
852	:param entry_node: lxml node ElementTree object to be appended to
853	"""
854	attr = {}
855	if datainfo.data.shape:
856	attr["x_bins"] = str(len(datainfo.x_bins))
857	attr["y_bins"] = str(len(datainfo.y_bins))
858	node = self.create_element("SASdata", attr)
859	self.append(node, entry_node)
860
861	point = self.create_element("Idata")
862	node.append(point)
863	qx = ','.join(str(v) for v in datainfo.qx_data)
864	qy = ','.join(str(v) for v in datainfo.qy_data)
865	intensity = ','.join(str(v) for v in datainfo.data)
866
867	self.write_node(point, "Qx", qx,
868	{'unit': datainfo._xunit})
869	self.write_node(point, "Qy", qy,
870	{'unit': datainfo._yunit})
871	self.write_node(point, "I", intensity,
872	{'unit': datainfo._zunit})
873	if datainfo.err_data is not None:
874	err = ','.join(str(v) for v in datainfo.err_data)
875	self.write_node(point, "Idev", err,
876	{'unit': datainfo._zunit})
877	if datainfo.dqy_data is not None:
878	dqy = ','.join(str(v) for v in datainfo.dqy_data)
879	self.write_node(point, "Qydev", dqy,
880	{'unit': datainfo._yunit})
881	if datainfo.dqx_data is not None:
882	dqx = ','.join(str(v) for v in datainfo.dqx_data)
883	self.write_node(point, "Qxdev", dqx,
884	{'unit': datainfo._xunit})
885	if datainfo.mask is not None:
886	mask = ','.join("1" if v else "0" for v in datainfo.mask)
887	self.write_node(point, "Mask", mask)
888
889	def _write_trans_spectrum(self, datainfo, entry_node):
890	"""
891	Writes the transmission spectrum data to the XML file
892
893	:param datainfo: The Data1D object the information is coming from
894	:param entry_node: lxml node ElementTree object to be appended to
895	"""
896	for i in range(len(datainfo.trans_spectrum)):
897	spectrum = datainfo.trans_spectrum[i]
898	node = self.create_element("SAStransmission_spectrum",
899	{"name" : spectrum.name})
900	self.append(node, entry_node)
901	if isinstance(spectrum.timestamp, datetime.datetime):
902	node.setAttribute("timestamp", spectrum.timestamp)
903	for i in range(len(spectrum.wavelength)):
904	point = self.create_element("Tdata")
905	node.append(point)
906	self.write_node(point, "Lambda", spectrum.wavelength[i],
907	{'unit': spectrum.wavelength_unit})
908	self.write_node(point, "T", spectrum.transmission[i],
909	{'unit': spectrum.transmission_unit})
910	if spectrum.transmission_deviation is not None \
911	and len(spectrum.transmission_deviation) >= i:
912	self.write_node(point, "Tdev",
913	spectrum.transmission_deviation[i],
914	{'unit':
915	spectrum.transmission_deviation_unit})
916
917	def _write_sample_info(self, datainfo, entry_node):
918	"""
919	Writes the sample information to the XML file
920
921	:param datainfo: The Data1D object the information is coming from
922	:param entry_node: lxml node ElementTree object to be appended to
923	"""
924	sample = self.create_element("SASsample")
925	if datainfo.sample.name is not None:
926	self.write_attribute(sample, "name",
927	str(datainfo.sample.name))
928	self.append(sample, entry_node)
929	self.write_node(sample, "ID", str(datainfo.sample.ID))
930	self.write_node(sample, "thickness", datainfo.sample.thickness,
931	{"unit": datainfo.sample.thickness_unit})
932	self.write_node(sample, "transmission", datainfo.sample.transmission)
933	self.write_node(sample, "temperature", datainfo.sample.temperature,
934	{"unit": datainfo.sample.temperature_unit})
935
936	pos = self.create_element("position")
937	written = self.write_node(pos,
938	"x",
939	datainfo.sample.position.x,
940	{"unit": datainfo.sample.position_unit})
941	written = written \| self.write_node( \
942	pos, "y", datainfo.sample.position.y,
943	{"unit": datainfo.sample.position_unit})
944	written = written \| self.write_node( \
945	pos, "z", datainfo.sample.position.z,
946	{"unit": datainfo.sample.position_unit})
947	if written == True:
948	self.append(pos, sample)
949
950	ori = self.create_element("orientation")
951	written = self.write_node(ori, "roll",
952	datainfo.sample.orientation.x,
953	{"unit": datainfo.sample.orientation_unit})
954	written = written \| self.write_node( \
955	ori, "pitch", datainfo.sample.orientation.y,
956	{"unit": datainfo.sample.orientation_unit})
957	written = written \| self.write_node( \
958	ori, "yaw", datainfo.sample.orientation.z,
959	{"unit": datainfo.sample.orientation_unit})
960	if written == True:
961	self.append(ori, sample)
962
963	for item in datainfo.sample.details:
964	self.write_node(sample, "details", item)
965
966	def _write_instrument(self, datainfo, entry_node):
967	"""
968	Writes the instrumental information to the XML file
969
970	:param datainfo: The Data1D object the information is coming from
971	:param entry_node: lxml node ElementTree object to be appended to
972	"""
973	instr = self.create_element("SASinstrument")
974	self.append(instr, entry_node)
975	self.write_node(instr, "name", datainfo.instrument)
976	return instr
977
978	def _write_source(self, datainfo, instr):
979	"""
980	Writes the source information to the XML file
981
982	:param datainfo: The Data1D object the information is coming from
983	:param instr: instrument node to be appended to
984	"""
985	source = self.create_element("SASsource")
986	if datainfo.source.name is not None:
987	self.write_attribute(source, "name",
988	str(datainfo.source.name))
989	self.append(source, instr)
990	if datainfo.source.radiation is None or datainfo.source.radiation == '':
991	datainfo.source.radiation = "neutron"
992	self.write_node(source, "radiation", datainfo.source.radiation)
993
994	size = self.create_element("beam_size")
995	if datainfo.source.beam_size_name is not None:
996	self.write_attribute(size, "name",
997	str(datainfo.source.beam_size_name))
998	written = self.write_node( \
999	size, "x", datainfo.source.beam_size.x,
1000	{"unit": datainfo.source.beam_size_unit})
1001	written = written \| self.write_node( \
1002	size, "y", datainfo.source.beam_size.y,
1003	{"unit": datainfo.source.beam_size_unit})
1004	written = written \| self.write_node( \
1005	size, "z", datainfo.source.beam_size.z,
1006	{"unit": datainfo.source.beam_size_unit})
1007	if written == True:
1008	self.append(size, source)
1009
1010	self.write_node(source, "beam_shape", datainfo.source.beam_shape)
1011	self.write_node(source, "wavelength",
1012	datainfo.source.wavelength,
1013	{"unit": datainfo.source.wavelength_unit})
1014	self.write_node(source, "wavelength_min",
1015	datainfo.source.wavelength_min,
1016	{"unit": datainfo.source.wavelength_min_unit})
1017	self.write_node(source, "wavelength_max",
1018	datainfo.source.wavelength_max,
1019	{"unit": datainfo.source.wavelength_max_unit})
1020	self.write_node(source, "wavelength_spread",
1021	datainfo.source.wavelength_spread,
1022	{"unit": datainfo.source.wavelength_spread_unit})
1023
1024	def _write_collimation(self, datainfo, instr):
1025	"""
1026	Writes the collimation information to the XML file
1027
1028	:param datainfo: The Data1D object the information is coming from
1029	:param instr: lxml node ElementTree object to be appended to
1030	"""
1031	if datainfo.collimation == [] or datainfo.collimation is None:
1032	coll = Collimation()
1033	datainfo.collimation.append(coll)
1034	for item in datainfo.collimation:
1035	coll = self.create_element("SAScollimation")
1036	if item.name is not None:
1037	self.write_attribute(coll, "name", str(item.name))
1038	self.append(coll, instr)
1039
1040	self.write_node(coll, "length", item.length,
1041	{"unit": item.length_unit})
1042
1043	for aperture in item.aperture:
1044	apert = self.create_element("aperture")
1045	if aperture.name is not None:
1046	self.write_attribute(apert, "name", str(aperture.name))
1047	if aperture.type is not None:
1048	self.write_attribute(apert, "type", str(aperture.type))
1049	self.append(apert, coll)
1050
1051	size = self.create_element("size")
1052	if aperture.size_name is not None:
1053	self.write_attribute(size, "name",
1054	str(aperture.size_name))
1055	written = self.write_node(size, "x", aperture.size.x,
1056	{"unit": aperture.size_unit})
1057	written = written \| self.write_node( \
1058	size, "y", aperture.size.y,
1059	{"unit": aperture.size_unit})
1060	written = written \| self.write_node( \
1061	size, "z", aperture.size.z,
1062	{"unit": aperture.size_unit})
1063	if written == True:
1064	self.append(size, apert)
1065
1066	self.write_node(apert, "distance", aperture.distance,
1067	{"unit": aperture.distance_unit})
1068
1069	def _write_detectors(self, datainfo, instr):
1070	"""
1071	Writes the detector information to the XML file
1072
1073	:param datainfo: The Data1D object the information is coming from
1074	:param inst: lxml instrument node to be appended to
1075	"""
1076	if datainfo.detector is None or datainfo.detector == []:
1077	det = Detector()
1078	det.name = ""
1079	datainfo.detector.append(det)
1080
1081	for item in datainfo.detector:
1082	det = self.create_element("SASdetector")
1083	written = self.write_node(det, "name", item.name)
1084	written = written \| self.write_node(det, "SDD", item.distance,
1085	{"unit": item.distance_unit})
1086	if written == True:
1087	self.append(det, instr)
1088
1089	off = self.create_element("offset")
1090	written = self.write_node(off, "x", item.offset.x,
1091	{"unit": item.offset_unit})
1092	written = written \| self.write_node(off, "y", item.offset.y,
1093	{"unit": item.offset_unit})
1094	written = written \| self.write_node(off, "z", item.offset.z,
1095	{"unit": item.offset_unit})
1096	if written == True:
1097	self.append(off, det)
1098
1099	ori = self.create_element("orientation")
1100	written = self.write_node(ori, "roll", item.orientation.x,
1101	{"unit": item.orientation_unit})
1102	written = written \| self.write_node(ori, "pitch",
1103	item.orientation.y,
1104	{"unit": item.orientation_unit})
1105	written = written \| self.write_node(ori, "yaw",
1106	item.orientation.z,
1107	{"unit": item.orientation_unit})
1108	if written == True:
1109	self.append(ori, det)
1110
1111	center = self.create_element("beam_center")
1112	written = self.write_node(center, "x", item.beam_center.x,
1113	{"unit": item.beam_center_unit})
1114	written = written \| self.write_node(center, "y",
1115	item.beam_center.y,
1116	{"unit": item.beam_center_unit})
1117	written = written \| self.write_node(center, "z",
1118	item.beam_center.z,
1119	{"unit": item.beam_center_unit})
1120	if written == True:
1121	self.append(center, det)
1122
1123	pix = self.create_element("pixel_size")
1124	written = self.write_node(pix, "x", item.pixel_size.x,
1125	{"unit": item.pixel_size_unit})
1126	written = written \| self.write_node(pix, "y", item.pixel_size.y,
1127	{"unit": item.pixel_size_unit})
1128	written = written \| self.write_node(pix, "z", item.pixel_size.z,
1129	{"unit": item.pixel_size_unit})
1130	if written == True:
1131	self.append(pix, det)
1132	self.write_node(det, "slit_length", item.slit_length,
1133	{"unit": item.slit_length_unit})
1134
1135
1136	def _write_process_notes(self, datainfo, entry_node):
1137	"""
1138	Writes the process notes to the XML file
1139
1140	:param datainfo: The Data1D object the information is coming from
1141	:param entry_node: lxml node ElementTree object to be appended to
1142
1143	"""
1144	for item in datainfo.process:
1145	node = self.create_element("SASprocess")
1146	self.append(node, entry_node)
1147	self.write_node(node, "name", item.name)
1148	self.write_node(node, "date", item.date)
1149	self.write_node(node, "description", item.description)
1150	for term in item.term:
1151	if isinstance(term, list):
1152	value = term['value']
1153	del term['value']
1154	elif isinstance(term, dict):
1155	value = term.get("value")
1156	del term['value']
1157	else:
1158	value = term
1159	self.write_node(node, "term", value, term)
1160	for note in item.notes:
1161	self.write_node(node, "SASprocessnote", note)
1162	if len(item.notes) == 0:
1163	self.write_node(node, "SASprocessnote", "")
1164
1165	def _write_notes(self, datainfo, entry_node):
1166	"""
1167	Writes the notes to the XML file and creates an empty note if none
1168	exist
1169
1170	:param datainfo: The Data1D object the information is coming from
1171	:param entry_node: lxml node ElementTree object to be appended to
1172
1173	"""
1174	if len(datainfo.notes) == 0:
1175	node = self.create_element("SASnote")
1176	self.append(node, entry_node)
1177	else:
1178	for item in datainfo.notes:
1179	node = self.create_element("SASnote")
1180	self.write_text(node, item)
1181	self.append(node, entry_node)
1182
1183	def _check_origin(self, entry_node, doc):
1184	"""
1185	Return the document, and the SASentry node associated with
1186	the data we just wrote.
1187	If the calling function was not the cansas reader, return a minidom
1188	object rather than an lxml object.
1189
1190	:param entry_node: lxml node ElementTree object to be appended to
1191	:param doc: entire xml tree
1192	"""
1193	if not self.frm:
1194	self.frm = inspect.stack()[1]
1195	mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
1196	mod_name = mod_name.replace(".py", "")
1197	mod = mod_name.split("sas/")
1198	mod_name = mod[1]
1199	if mod_name != "sascalc/dataloader/readers/cansas_reader":
1200	string = self.to_string(doc, pretty_print=False)
1201	doc = parseString(string)
1202	node_name = entry_node.tag
1203	node_list = doc.getElementsByTagName(node_name)
1204	entry_node = node_list.item(0)
1205	return doc, entry_node
1206
1207	# DO NOT REMOVE - used in saving and loading panel states.
1208	def _store_float(self, location, node, variable, storage, optional=True):
1209	"""
1210	Get the content of a xpath location and store
1211	the result. Check that the units are compatible
1212	with the destination. The value is expected to
1213	be a float.
1214
1215	The xpath location might or might not exist.
1216	If it does not exist, nothing is done
1217
1218	:param location: xpath location to fetch
1219	:param node: node to read the data from
1220	:param variable: name of the data member to store it in [string]
1221	:param storage: data object that has the 'variable' data member
1222	:param optional: if True, no exception will be raised
1223	if unit conversion can't be done
1224
1225	:raise ValueError: raised when the units are not recognized
1226	"""
1227	entry = get_content(location, node)
1228	try:
1229	value = float(entry.text)
1230	except ValueError:
1231	value = None
1232
1233	if value is not None:
1234	# If the entry has units, check to see that they are
1235	# compatible with what we currently have in the data object
1236	units = entry.get('unit')
1237	if units is not None:
1238	toks = variable.split('.')
1239	local_unit = getattr(storage, toks[0]+"_unit")
1240	if local_unit is not None and units.lower() != local_unit.lower():
1241	try:
1242	conv = Converter(units)
1243	setattrchain(storage, variable, conv(value, units=local_unit))
1244	except Exception:
1245	_, exc_value, _ = sys.exc_info()
1246	err_mess = "CanSAS reader: could not convert"
1247	err_mess += " %s unit [%s]; expecting [%s]\n %s" \
1248	% (variable, units, local_unit, exc_value)
1249	self.errors.add(err_mess)
1250	if optional:
1251	logger.info(err_mess)
1252	else:
1253	raise ValueError(err_mess)
1254	else:
1255	setattrchain(storage, variable, value)
1256	else:
1257	setattrchain(storage, variable, value)
1258
1259	# DO NOT REMOVE - used in saving and loading panel states.
1260	def _store_content(self, location, node, variable, storage):
1261	"""
1262	Get the content of a xpath location and store
1263	the result. The value is treated as a string.
1264
1265	The xpath location might or might not exist.
1266	If it does not exist, nothing is done
1267
1268	:param location: xpath location to fetch
1269	:param node: node to read the data from
1270	:param variable: name of the data member to store it in [string]
1271	:param storage: data object that has the 'variable' data member
1272
1273	:return: return a list of errors
1274	"""
1275	entry = get_content(location, node)
1276	if entry is not None and entry.text is not None:
1277	setattrchain(storage, variable, entry.text.strip())
1278
1279	# DO NOT REMOVE Called by outside packages:
1280	# sas.sasgui.perspectives.invariant.invariant_state
1281	# sas.sasgui.perspectives.fitting.pagestate
1282	def get_content(location, node):
1283	"""
1284	Get the first instance of the content of a xpath location.
1285
1286	:param location: xpath location
1287	:param node: node to start at
1288
1289	:return: Element, or None
1290	"""
1291	nodes = node.xpath(location,
1292	namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
1293	if len(nodes) > 0:
1294	return nodes[0]
1295	else:
1296	return None
1297
1298	# DO NOT REMOVE Called by outside packages:
1299	# sas.sasgui.perspectives.fitting.pagestate
1300	def write_node(doc, parent, name, value, attr=None):
1301	"""
1302	:param doc: document DOM
1303	:param parent: parent node
1304	:param name: tag of the element
1305	:param value: value of the child text node
1306	:param attr: attribute dictionary
1307
1308	:return: True if something was appended, otherwise False
1309	"""
1310	if attr is None:
1311	attr = {}
1312	if value is not None:
1313	node = doc.createElement(name)
1314	node.appendChild(doc.createTextNode(str(value)))
1315	for item in attr:
1316	node.setAttribute(item, attr[item])
1317	parent.appendChild(node)
1318	return True
1319	return False
1320
1321	def getattrchain(obj, chain, default=None):
1322	"""Like getattr, but the attr may contain multiple parts separated by '.'"""
1323	for part in chain.split('.'):
1324	if hasattr(obj, part):
1325	obj = getattr(obj, part, None)
1326	else:
1327	return default
1328	return obj
1329
1330	def setattrchain(obj, chain, value):
1331	"""Like setattr, but the attr may contain multiple parts separated by '.'"""
1332	parts = list(chain.split('.'))
1333	for part in parts[-1]:
1334	obj = getattr(obj, part, None)
1335	if obj is None:
1336	raise ValueError("missing parent object "+part)
1337	setattr(obj, value)

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SasView

source: sasview/src/sas/sascalc/dataloader/readers/cansas_reader.py @ 18f11a6

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